Breast cancer is the most common malignancy in American women, yet its molecular pathogenesis remains elusive. This exploratory study is designed to identify the genetic changes that are responsible for driving a mammary neoplasm from the in situ to the invasive stage, and it addresses several aspects of PA-03-003 issued by the NCI. It is prompted by the marked pathologic and clinical heterogeneity of ductal carcinoma in situ (DCIS). Among low grade DCIS (LGDCIS) lesions, only a minority have the capacity to progress to an invasive carcinoma, but currently they cannot be distinguished from the great majority of clinically indolent LGDCIS. Therefore, the latter tend to be over-treated, to the detriment of many women. We propose to apply state-of-the-art array comparative genomic hybridization (aCGH) technology utilizing high resolution BAC arrays developed at the Roswell Park Cancer Institute to 35 micro dissected non-recurrent LGDCIS and 35 size matched LGDCIS cases associated with an invasive component. We expect that this analysis will reveal a number of DNA copy number aberrations (CNAs) that distinguish indolent from potentially aggressive DCIS (Aim 1). Moreover, the 30 mixed carcinomas will be further analyzed for CNAs that distinguish the invasive from the in situ component (Aim 2). In a series of validation experiments, we will then confirm the abnormal copy number and expression level of candidate genes discovered by the aCGH analysis (Aim 3). This study combines expert morphologic analysis and cutting edge molecular technology to tackle a significant clinical problem, namely, the identification of DCIS cases that do not require treatment beyond the initial surgical excision. In addition, it will fill important gaps in our knowledge of the molecular pathology of early breast cancer, particularly by identifying CNAs in LGDCIS and by identifying chromosomal loci and genes that determine stromal invasion. In the process, we expect to uncover novel diagnostic, prognostic, and predictive markers and new targets of breast cancer prevention and therapy. Lastly, our study explores the utility of high resolution aCGH as a clinically useful assay.